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  <h1>Source code for pymatgen.io.cssr</h1><div class="highlight"><pre>
<span></span><span class="c1"># coding: utf-8</span>
<span class="c1"># Copyright (c) Pymatgen Development Team.</span>
<span class="c1"># Distributed under the terms of the MIT License.</span>


<span class="sd">&quot;&quot;&quot;</span>
<span class="sd">This module provides input and output from the CSSR file format.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">re</span>

<span class="kn">from</span> <span class="nn">monty.io</span> <span class="kn">import</span> <span class="n">zopen</span>
<span class="kn">from</span> <span class="nn">pymatgen.core.lattice</span> <span class="kn">import</span> <span class="n">Lattice</span>
<span class="kn">from</span> <span class="nn">pymatgen.core.structure</span> <span class="kn">import</span> <span class="n">Structure</span>

<span class="n">__author__</span> <span class="o">=</span> <span class="s2">&quot;Shyue Ping Ong&quot;</span>
<span class="n">__copyright__</span> <span class="o">=</span> <span class="s2">&quot;Copyright 2012, The Materials Project&quot;</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;0.1&quot;</span>
<span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">&quot;Shyue Ping Ong&quot;</span>
<span class="n">__email__</span> <span class="o">=</span> <span class="s2">&quot;shyuep@gmail.com&quot;</span>
<span class="n">__date__</span> <span class="o">=</span> <span class="s2">&quot;Jan 24, 2012&quot;</span>


<div class="viewcode-block" id="Cssr"><a class="viewcode-back" href="../../../pymatgen.io.cssr.html#pymatgen.io.cssr.Cssr">[docs]</a><span class="k">class</span> <span class="nc">Cssr</span><span class="p">:</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Basic object for working with Cssr file. Right now, only conversion from</span>
<span class="sd">    a Structure to a Cssr file is supported.</span>
<span class="sd">    &quot;&quot;&quot;</span>

    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Args:</span>
<span class="sd">            structure (Structure/IStructure): A structure to create the Cssr object.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">if</span> <span class="ow">not</span> <span class="n">structure</span><span class="o">.</span><span class="n">is_ordered</span><span class="p">:</span>
            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;Cssr file can only be constructed from ordered &quot;</span>
                             <span class="s2">&quot;structure&quot;</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="n">structure</span>

    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="n">output</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;</span><span class="si">{:.4f}</span><span class="s2"> </span><span class="si">{:.4f}</span><span class="s2"> </span><span class="si">{:.4f}</span><span class="s2">&quot;</span>
                  <span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">abc</span><span class="p">),</span>
                  <span class="s2">&quot;</span><span class="si">{:.2f}</span><span class="s2"> </span><span class="si">{:.2f}</span><span class="s2"> </span><span class="si">{:.2f}</span><span class="s2"> SPGR =  1 P 1    OPT = 1&quot;</span>
                  <span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">angles</span><span class="p">),</span>
                  <span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> 0&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">)),</span>
                  <span class="s2">&quot;0 </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">formula</span><span class="p">)]</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">site</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">sites</span><span class="p">):</span>
            <span class="n">output</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> </span><span class="si">{}</span><span class="s2"> </span><span class="si">{:.4f}</span><span class="s2"> </span><span class="si">{:.4f}</span><span class="s2"> </span><span class="si">{:.4f}</span><span class="s2">&quot;</span>
                          <span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">site</span><span class="o">.</span><span class="n">specie</span><span class="p">,</span> <span class="n">site</span><span class="o">.</span><span class="n">a</span><span class="p">,</span> <span class="n">site</span><span class="o">.</span><span class="n">b</span><span class="p">,</span> <span class="n">site</span><span class="o">.</span><span class="n">c</span><span class="p">))</span>
        <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>

<div class="viewcode-block" id="Cssr.write_file"><a class="viewcode-back" href="../../../pymatgen.io.cssr.html#pymatgen.io.cssr.Cssr.write_file">[docs]</a>    <span class="k">def</span> <span class="nf">write_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Write out a CSSR file.</span>

<span class="sd">        Args:</span>
<span class="sd">            filename (str): Filename to write to.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">with</span> <span class="n">zopen</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;wt&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span></div>

<div class="viewcode-block" id="Cssr.from_string"><a class="viewcode-back" href="../../../pymatgen.io.cssr.html#pymatgen.io.cssr.Cssr.from_string">[docs]</a>    <span class="nd">@staticmethod</span>
    <span class="k">def</span> <span class="nf">from_string</span><span class="p">(</span><span class="n">string</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Reads a string representation to a Cssr object.</span>

<span class="sd">        Args:</span>
<span class="sd">            string (str): A string representation of a CSSR.</span>

<span class="sd">        Returns:</span>
<span class="sd">            Cssr object.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="n">lines</span> <span class="o">=</span> <span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
        <span class="n">toks</span> <span class="o">=</span> <span class="n">lines</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="n">lengths</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">toks</span><span class="p">]</span>
        <span class="n">toks</span> <span class="o">=</span> <span class="n">lines</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="n">angles</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">3</span><span class="p">]]</span>
        <span class="n">latt</span> <span class="o">=</span> <span class="n">Lattice</span><span class="o">.</span><span class="n">from_parameters</span><span class="p">(</span><span class="o">*</span><span class="n">lengths</span><span class="p">,</span> <span class="o">*</span><span class="n">angles</span><span class="p">)</span>
        <span class="n">sp</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="n">coords</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">[</span><span class="mi">4</span><span class="p">:]:</span>
            <span class="n">m</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
                <span class="sa">r</span><span class="s2">&quot;\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)&quot;</span><span class="p">,</span>
                <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
            <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
                <span class="n">sp</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
                <span class="n">coords</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="n">i</span><span class="p">))</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">)])</span>
        <span class="k">return</span> <span class="n">Cssr</span><span class="p">(</span><span class="n">Structure</span><span class="p">(</span><span class="n">latt</span><span class="p">,</span> <span class="n">sp</span><span class="p">,</span> <span class="n">coords</span><span class="p">))</span></div>

<div class="viewcode-block" id="Cssr.from_file"><a class="viewcode-back" href="../../../pymatgen.io.cssr.html#pymatgen.io.cssr.Cssr.from_file">[docs]</a>    <span class="nd">@staticmethod</span>
    <span class="k">def</span> <span class="nf">from_file</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Reads a CSSR file to a Cssr object.</span>

<span class="sd">        Args:</span>
<span class="sd">            filename (str): Filename to read from.</span>

<span class="sd">        Returns:</span>
<span class="sd">            Cssr object.</span>
<span class="sd">        &quot;&quot;&quot;</span>
        <span class="k">with</span> <span class="n">zopen</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s2">&quot;rt&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
            <span class="k">return</span> <span class="n">Cssr</span><span class="o">.</span><span class="n">from_string</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">())</span></div></div>
</pre></div>

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